[2024-01-25 18:09:50,571] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:50,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:50,573] [INFO] DQC Reference Directory: /var/lib/cwl/stg6053cd96-598a-4f0e-a026-44594b735deb/dqc_reference
[2024-01-25 18:09:51,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:51,789] [INFO] Task started: Prodigal
[2024-01-25 18:09:51,789] [INFO] Running command: gunzip -c /var/lib/cwl/stga8fb6e06-a3c0-4b39-86a6-6044ae0a5bfb/GCF_027497495.1_ASM2749749v1_genomic.fna.gz | prodigal -d GCF_027497495.1_ASM2749749v1_genomic.fna/cds.fna -a GCF_027497495.1_ASM2749749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:13,539] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:13,539] [INFO] Task started: HMMsearch
[2024-01-25 18:10:13,540] [INFO] Running command: hmmsearch --tblout GCF_027497495.1_ASM2749749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6053cd96-598a-4f0e-a026-44594b735deb/dqc_reference/reference_markers.hmm GCF_027497495.1_ASM2749749v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:13,870] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:13,871] [INFO] Found 6/6 markers.
[2024-01-25 18:10:13,927] [INFO] Query marker FASTA was written to GCF_027497495.1_ASM2749749v1_genomic.fna/markers.fasta
[2024-01-25 18:10:13,928] [INFO] Task started: Blastn
[2024-01-25 18:10:13,928] [INFO] Running command: blastn -query GCF_027497495.1_ASM2749749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6053cd96-598a-4f0e-a026-44594b735deb/dqc_reference/reference_markers.fasta -out GCF_027497495.1_ASM2749749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:15,212] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:15,215] [INFO] Selected 17 target genomes.
[2024-01-25 18:10:15,215] [INFO] Target genome list was writen to GCF_027497495.1_ASM2749749v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:15,238] [INFO] Task started: fastANI
[2024-01-25 18:10:15,238] [INFO] Running command: fastANI --query /var/lib/cwl/stga8fb6e06-a3c0-4b39-86a6-6044ae0a5bfb/GCF_027497495.1_ASM2749749v1_genomic.fna.gz --refList GCF_027497495.1_ASM2749749v1_genomic.fna/target_genomes.txt --output GCF_027497495.1_ASM2749749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:52,166] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:52,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6053cd96-598a-4f0e-a026-44594b735deb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:52,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6053cd96-598a-4f0e-a026-44594b735deb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:52,178] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:10:52,178] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:52,178] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Streptomyces tubercidicus	strain=NBRC 13090	GCA_009811635.1	47759	47759	type	True	99.9986	2633	2761	95	conclusive
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	92.562	2180	2761	95	below_threshold
Streptomyces glebosus	strain=NBRC 13786	GCA_009811575.1	249580	249580	type	True	92.4913	2165	2761	95	below_threshold
Streptomyces libani subsp. libani	strain=NBRC 13452	GCA_009811595.1	68044	68043	type	True	92.4069	2248	2761	95	below_threshold
Streptomyces platensis	strain=ATCC 23948	GCA_008704855.1	58346	58346	type	True	92.3988	2166	2761	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	92.3792	2118	2761	95	below_threshold
Streptomyces libani subsp. libani	strain=JCM 4322	GCA_014649275.1	68044	68043	type	True	92.3028	2230	2761	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_019880305.1	249567	249567	type	True	89.7478	2065	2761	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	89.7202	1978	2761	95	below_threshold
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	89.4604	2101	2761	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	89.3935	2094	2761	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	88.6148	1936	2761	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	85.3213	1583	2761	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	84.5039	1258	2761	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.7303	1604	2761	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.672	1560	2761	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.6456	1618	2761	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:52,180] [INFO] DFAST Taxonomy check result was written to GCF_027497495.1_ASM2749749v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:52,181] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:52,182] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:52,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6053cd96-598a-4f0e-a026-44594b735deb/dqc_reference/checkm_data
[2024-01-25 18:10:52,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:52,260] [INFO] Task started: CheckM
[2024-01-25 18:10:52,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027497495.1_ASM2749749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027497495.1_ASM2749749v1_genomic.fna/checkm_input GCF_027497495.1_ASM2749749v1_genomic.fna/checkm_result
[2024-01-25 18:12:52,769] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:52,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:52,806] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:52,806] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:52,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027497495.1_ASM2749749v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:52,809] [INFO] Task started: Blastn
[2024-01-25 18:12:52,809] [INFO] Running command: blastn -query GCF_027497495.1_ASM2749749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6053cd96-598a-4f0e-a026-44594b735deb/dqc_reference/reference_markers_gtdb.fasta -out GCF_027497495.1_ASM2749749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:54,954] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:54,959] [INFO] Selected 8 target genomes.
[2024-01-25 18:12:54,959] [INFO] Target genome list was writen to GCF_027497495.1_ASM2749749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:54,971] [INFO] Task started: fastANI
[2024-01-25 18:12:54,971] [INFO] Running command: fastANI --query /var/lib/cwl/stga8fb6e06-a3c0-4b39-86a6-6044ae0a5bfb/GCF_027497495.1_ASM2749749v1_genomic.fna.gz --refList GCF_027497495.1_ASM2749749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027497495.1_ASM2749749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:13,678] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:13,685] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:13,685] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_009811635.1	s__Streptomyces tubercidicus	99.9986	2635	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009811595.1	s__Streptomyces libani	92.4048	2247	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.04	96.45	0.91	0.86	12	-
GCF_008704855.1	s__Streptomyces platensis	92.3924	2165	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	-
GCF_001270575.1	s__Streptomyces decoyicus	89.7252	1977	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_009811555.1	s__Streptomyces caniferus	89.4637	2102	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187385.1	s__Streptomyces sp900187385	89.4333	2024	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.51	0.98	0.96	9	-
GCF_004125265.1	s__Streptomyces lydicus_C	89.3707	2041	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176265.1	s__Streptomyces angustmyceticus	89.3609	2043	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:13,686] [INFO] GTDB search result was written to GCF_027497495.1_ASM2749749v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:13,687] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:13,689] [INFO] DFAST_QC result json was written to GCF_027497495.1_ASM2749749v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:13,690] [INFO] DFAST_QC completed!
[2024-01-25 18:13:13,690] [INFO] Total running time: 0h3m23s